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Zhao R, Wang Y, Gao J, Zhang J. Method and Implementation of Projected Hybrid Orbitals for Treating Multiple Covalent Bonds in Combined QM/MM Calculations. J Chem Theory Comput 2024; 20:10574-10587. [PMID: 39589229 DOI: 10.1021/acs.jctc.4c01326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2024]
Abstract
The projected hybrid orbital (PHO) method for treatment of multiple boundary atoms introduces a novel solution for handling the covalent connection between quantum mechanical (QM) and molecular mechanical (MM) regions in QM/MM calculations. By projecting the QM basis, typically adequately large for computational accuracy, onto a secondary minimal basis set on the boundary atom, it preserves electronic interactions between the two regions without system-specific parameters. Applicable in both ab initio wave function theory and density functional theory, PHO has been shown to maintain structural and electronic integrity across various systems. It offers key advantages over traditional QM/MM methods, such as avoiding modification of MM charge distribution and energy corrections, while being flexible for biochemical systems and potentially broader QM/QM embedding frameworks.
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Affiliation(s)
- Ruoqi Zhao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Yingjie Wang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jun Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
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Song Y, Huang W, Liu C, Lei Y, Suo B, Ma H. Spin-Adapted Externally Contracted Multireference Configuration Interaction Method Based on Selected Reference Configurations. J Phys Chem A 2024; 128:958-971. [PMID: 38272019 DOI: 10.1021/acs.jpca.3c07526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
As one kind of approximation of the full configuration interaction solution, the selected configuration interaction (sCI) methods have been shown to be valuable for large active spaces. However, the inclusion of dynamic correlation beyond large active spaces is necessary for more quantitative results. Since the sCI wave function can provide a compact reference for multireference methods, previously, we proposed an externally contracted multireference configuration interaction method using the sCI reference reconstructed from the density matrix renormalization group wave function [J. Chem. Theory Comput. 2018, 14, 4747-4755]. The DMRG2sCI-EC-MRCI method is promising for dealing with more than 30 active orbitals and large basis sets. However, it suffers from two drawbacks: spin contamination and low efficiency when using Slater determinant bases. To solve these problems, in this work, we adopt configuration state function bases and introduce a new algorithm based on the hybrid of tree structure for convenient configuration space management and the graphical unitary group approach for efficient matrix element calculation. The test calculation of naphthalene shows that the spin-adapted version could achieve a speed-up of 6.0 compared with the previous version based on the Slater determinant. Examples of dinuclear copper(II) compound as well as Ln(III) and An(III) complexes show that the sCI-EC-MRCI can give quantitatively accurate results by including dynamic correlation over sCI for systems with large active spaces and basis sets.
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Affiliation(s)
- Yinxuan Song
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Wei Huang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Chungen Liu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yibo Lei
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Shaanxi Key Laboratory of Physico-Inorganic Chemistry, Northwest University, Xi'an 710127, People's Republic of China
| | - Bingbing Suo
- Shaanxi Key Laboratory for Theoretical Physics Frontiers, Institute of Modern Physics, Northwest University, Xi'an 710127, People's Republic of China
| | - Haibo Ma
- Qingdao Institute for Theoretical and Computational Sciences, Qingdao Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
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Chen WK, Fang WH, Cui G. Extending multi-layer energy-based fragment method for excited-state calculations of large covalently bonded fragment systems. J Chem Phys 2023; 158:044110. [PMID: 36725521 DOI: 10.1063/5.0129458] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recently, we developed a low-scaling Multi-Layer Energy-Based Fragment (MLEBF) method for accurate excited-state calculations and nonadiabatic dynamics simulations of nonbonded fragment systems. In this work, we extend the MLEBF method to treat covalently bonded fragment ones. The main idea is cutting a target system into many fragments according to chemical properties. Fragments with dangling bonds are first saturated by chemical groups; then, saturated fragments, together with the original fragments without dangling bonds, are grouped into different layers. The accurate total energy expression is formulated with the many-body energy expansion theory, in combination with the inclusion-exclusion principle that is used to delete the contribution of chemical groups introduced to saturate dangling bonds. Specifically, in a two-layer MLEBF model, the photochemically active and inert layers are calculated with high-level and efficient electronic structure methods, respectively. Intralayer and interlayer energies can be truncated at the two- or three-body interaction level. Subsequently, through several systems, including neutral and charged covalently bonded fragment systems, we demonstrate that MLEBF can provide accurate ground- and excited-state energies and gradients. Finally, we realize the structure, conical intersection, and path optimizations by combining our MLEBF program with commercial and free packages, e.g., ASE and SciPy. These developments make MLEBF a practical and reliable tool for studying complex photochemical and photophysical processes of large nonbonded and bonded fragment systems.
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Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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Liu W. Perspective: Simultaneous treatment of relativity, correlation, and
QED. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science Shandong University Qingdao Shandong China
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Li J, Wu C, Lei Y, Liu W. Tuning Catalyst-Free Photocontrolled Polymerization by Substitution: A Quantitative and Qualitative Interpretation. J Phys Chem Lett 2022; 13:3290-3296. [PMID: 35389216 DOI: 10.1021/acs.jpclett.2c00830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Catalyst-free photocontrolled reversible addition-fragmentation chain transfer (RAFT) polymerization avoids the side effects of photocatalysts but has the accompanying slow kinetics, thereby warranting more efficient photolysis and faster chain transfer. To understand the underlying mechanisms, both quantitative and qualitative interpretations are needed. Such a goal can be achieved by the iCAS (imposed automatic selection and localization of complete active spaces) approach [J. Chem. Theory Comput. 2021, 17, 4846], which maintains the same CAS and meanwhile provides localized orbitals along the whole reaction. Taking dithiobenzoate as a representative of RAFT agents, it is found here that electron-donating substitution (by methoxy) clearly outperforms both electron-standing (by methyl) and electron-withdrawing (by cyano) substitutions in facilitating photo-RAFT polymerization, by narrowing the gap between the π* and σ* orbitals, so as to facilitate the π* → σ* charge transfer dominating both the photolysis and chain transfer processes. Such findings are of general values.
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Affiliation(s)
- Jun Li
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China
| | - Chenyu Wu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China
| | - Yibo Lei
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Shaanxi key Laboratory of Physico-Inorganic Chemistry, Northwest University, Xi'an 710127, Shaanxi, P. R. China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China
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Guo Y, Zhang N, Lei Y, Liu W. iCISCF: An Iterative Configuration Interaction-Based Multiconfigurational Self-Consistent Field Theory for Large Active Spaces. J Chem Theory Comput 2021; 17:7545-7561. [PMID: 34757746 DOI: 10.1021/acs.jctc.1c00781] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An iterative configuration interaction (iCI)-based multiconfigurational self-consistent field (SCF) theory, iCISCF, is proposed to handle systems that require large active spaces. The success of iCISCF stems from three ingredients: (1) efficient selection of individual configuration state functions spanning the active space while maintaining full spin symmetry; (2) the use of Jacobi rotation for optimization of the active orbitals in conjunction with a quasi-Newton algorithm for the core/active-virtual and core-active orbital rotations; (3) a second-order perturbative treatment of the residual space left over by the selection procedure (i.e., iCISCF(2)). Several examples that go beyond the capability of CASSCF are taken as showcases to reveal the efficacy of iCISCF and iCISCF(2), facilitated by iCAS for imposed automatic selection and localization of active orbitals.
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Affiliation(s)
- Yang Guo
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Ning Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yibo Lei
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Shaanxi Key Laboratory of Physico-Inorganic Chemistry, Northwest University, Xi'an, Shaanxi 710127, China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
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Lei Y, Suo B, Liu W. iCAS: Imposed Automatic Selection and Localization of Complete Active Spaces. J Chem Theory Comput 2021; 17:4846-4859. [PMID: 34314180 DOI: 10.1021/acs.jctc.1c00456] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
It is shown that in the spirit of "from fragments to molecule" for localizing molecular orbitals [J. Chem. Theory Comput. 2011, 7, 3643], a prechosen set of occupied/virtual valence/core atomic/fragmental orbitals can be transformed to an equivalent set of localized occupied/virtual pre-localized molecular orbitals (pre-LMO), which can then be taken as probes to select the same number of maximally matching localized occupied/virtual Hartree-Fock (HF) or restricted open-shell HF (ROHF) molecular orbitals as the initial local orbitals spanning the desired complete active space (CAS). In each cycle of the self-consistent field (SCF) calculation, the CASSCF orbitals can be localized by means of the noniterative "top-down least-change" algorithm for localizing ROHF orbitals [J. Chem. Phys. 2017, 146, 104104] such that the maximum matching between the orbitals of two adjacent iterations can readily be monitored, leading finally to converged localized CASSCF orbitals that overlap most the guess orbitals. Such an approach is to be dubbed as "imposed CASSCF" (iCASSCF or simply iCAS in short) for good reasons: (1) it has been assumed that only those electronic states that have largest projections onto the active space defined by the prechosen atomic/fragmental orbitals are to be targeted. This is certainly an imposed constraint but has wide applications in organic and transition metal chemistry where valence (or core) atomic/fragmental orbitals can readily be identified. (2) The selection of both initial and optimized local active orbitals is imposed from the very beginning by the pre-LMOs (which span the same space as the prechosen atomic/fragmental orbitals). Apart from the (imposed) automation and localization, iCAS has two additional merits: (a) the guess orbitals are guaranteed to be the same for all geometries, for the pre-LMOs do not change in character with geometry and (b) the use of localized orbitals facilitates the SCF convergence, particularly for large active spaces. Both organic molecules and transition-metal complexes are taken as showcases to reveal the efficacy of iCAS.
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Affiliation(s)
- Yibo Lei
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Shaanxi Key Laboratory of Physico-Inorganic Chemistry, Northwest University, Xi'an 710127, Shaanxi, P. R. China
| | - Bingbing Suo
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi'an 710127, Shaanxi, P. R. China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China
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